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Dindel specifications


Unique identifier OMICS_00096
Name Dindel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped Illumina read data
Input format BAM
Output data Variant calls
Output format VCF
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Cornelis Albers

Publication for Dindel

Dindel citations


Optimized detection of insertions/deletions (INDELs) in whole exome sequencing data

PLoS One
PMCID: 5549930
PMID: 28792971
DOI: 10.1371/journal.pone.0182272
call_split See protocol

[…] (http://picard.Sourceforget.net).WES data were analyzed using four INDEL calling algorithms, (1) GATK (http://www.broadinstitute.org/gatk/) [], (2) SAMtools (http://samtools.sourceforge.net/) [], (3) Dindel [], and (4) Freebayes [], following the guidelines provided in the user manuals. INDELs were called with each algorithm and the variants annotated using the ANNOVAR program (http://www.openbioi […]


Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations

Nat Commun
PMCID: 5474888
PMID: 28429735
DOI: 10.1038/ncomms14944

[…] s. Duplicate reads were removed using Picard tools. Base recalibration, local realignment around indels and SNV calling were performed using the GenomeAnalysisToolKit (GATK). Indels were called using Dindel. Mutations were filtered based on mapping quality, and sequencing coverage. Somatic mutations were further filtered by comparison with the matched germline reference and using common variant da […]


A human immunodeficiency syndrome caused by mutations in CARMIL2

Nat Commun
PMCID: 5473639
PMID: 28112205
DOI: 10.1038/ncomms14209
call_split See protocol

[…] ere removed using SAMtools version 1.18 (ref. ). SAMtools was also used to call SNPs with the command: ‘mpileup –M 300 –I –g –D -C50 –S'. Small insertions and deletions (indels) were identified using DinDel version 1.01 (ref. ), by first identifying putative indels for each sample Individually, and then re-running the DinDel on the pooled set of samples from family A with the previously identified […]


A mutation of EPT1 (SELENOI) underlies a new disorder of Kennedy pathway phospholipid biosynthesis

PMCID: 5382949
PMID: 28052917
DOI: 10.1093/brain/aww318

[…] otein Variation Effect Analyzer) (http://provean.jcvi.org/index.php)dbSNP (http://www.ncbi.nlm.nih.gov/SNP/)1000 Genomes Project (http://www.1000genomes.org/)GATK (http://www.broadinstitute.org/gatk/)Dindel (https://www.sanger.ac.uk/resources/software/dindel/)SNP Effect Predictor (http://www.ensembl.org/info/docs/tools/vep/index.html)Exome Aggregation Consortium (ExAC) Browser (http://exac.broadin […]


Characterization of ADME gene variation in 21 populations by exome sequencing

Pharmacogenet Genomics
PMCID: 5287433
PMID: 27984508
DOI: 10.1097/FPC.0000000000000260

[…] available array-based genotypes for six 1000G samples (Table S4, Supplemental digital content 1, http://links.lww.com/FPC/B140). Indel sites were discovered from the NEAVA samples (N=251) using both Dindel and the GATK v2.1-12 UnifiedGenotyper tool , and then, genotypes were called for the 1432 joint samples using the UnifiedGenotyper tool at the indel sites identified from the NEAVA samples. CN […]


Mutations in human C2CD3 cause skeletal dysplasia and provide new insights into phenotypic and cellular consequences of altered C2CD3 function

Sci Rep
PMCID: 4837335
PMID: 27094867
DOI: 10.1038/srep24083

[…] “splicing”, “frameshift substitution”, “stopgain SNV”, “stoploss SNV”) with minor allele frequency <0.005 (based on NCBI dbSNP (release 135), 1000 Genomes, 1000 Genomes small indels (called using the DINDEL programme), the SNPs of 46Genomes release by Complete Genomics, and whole exome data from over 2000 samples run internally using similar capture technology), were retained. As this family was n […]


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Dindel institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK

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